GeneNetworkBuilder: Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data

Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.

AuthorJianhong Ou , Haibo Liu, Heidi A Tissenbaum and Lihua Julie Zhu
Date of publicationNone
MaintainerJianhong Ou <jianhong.ou@umassmed.edu>
LicenseGPL (>= 2)
Version1.16.0

View on Bioconductor

Files in this package

GeneNetworkBuilder/.BBSoptions
GeneNetworkBuilder/DESCRIPTION
GeneNetworkBuilder/NAMESPACE
GeneNetworkBuilder/NEWS
GeneNetworkBuilder/R
GeneNetworkBuilder/R/GeneNetworkBuilder.R GeneNetworkBuilder/R/applications.R
GeneNetworkBuilder/build
GeneNetworkBuilder/build/vignette.rds
GeneNetworkBuilder/data
GeneNetworkBuilder/data/ce.IDsMap.rda
GeneNetworkBuilder/data/ce.interactionmap.rda
GeneNetworkBuilder/data/ce.mapIDs.rda
GeneNetworkBuilder/data/ce.miRNA.map.rda
GeneNetworkBuilder/data/datalist
GeneNetworkBuilder/data/example.data.rda
GeneNetworkBuilder/data/hs.IDsMap.rda
GeneNetworkBuilder/data/hs.interactionmap.rda
GeneNetworkBuilder/data/hs.mapIDs.rda
GeneNetworkBuilder/data/hs.miRNA.map.rda
GeneNetworkBuilder/inst
GeneNetworkBuilder/inst/doc
GeneNetworkBuilder/inst/doc/GeneNetworkBuilder.R
GeneNetworkBuilder/inst/doc/GeneNetworkBuilder.Rnw
GeneNetworkBuilder/inst/doc/GeneNetworkBuilder.pdf
GeneNetworkBuilder/inst/unitTests
GeneNetworkBuilder/inst/unitTests/test_geneNetworkBuilder.R
GeneNetworkBuilder/man
GeneNetworkBuilder/man/buildNetwork.Rd GeneNetworkBuilder/man/ce.IDsMap.Rd GeneNetworkBuilder/man/ce.interactionmap.Rd GeneNetworkBuilder/man/ce.mapIDs.Rd GeneNetworkBuilder/man/ce.miRNA.map.Rd GeneNetworkBuilder/man/convertID.Rd GeneNetworkBuilder/man/example.data.Rd GeneNetworkBuilder/man/filterNetwork.Rd GeneNetworkBuilder/man/hs.IDsMap.Rd GeneNetworkBuilder/man/hs.interactionmap.Rd GeneNetworkBuilder/man/hs.mapIDs.Rd GeneNetworkBuilder/man/hs.miRNA.map.Rd GeneNetworkBuilder/man/polishNetwork.Rd GeneNetworkBuilder/man/uniqueExprsData.Rd
GeneNetworkBuilder/src
GeneNetworkBuilder/src/Makevars
GeneNetworkBuilder/src/Makevars.win
GeneNetworkBuilder/src/geneTree.cpp
GeneNetworkBuilder/src/geneTree.h
GeneNetworkBuilder/src/nodefilter.cpp
GeneNetworkBuilder/tests
GeneNetworkBuilder/tests/runTests.R
GeneNetworkBuilder/vignettes
GeneNetworkBuilder/vignettes/GeneNetworkBuilder.Rnw
GeneNetworkBuilder/vignettes/hs_sample_rcytoscape.eps
GeneNetworkBuilder/vignettes/hs_sample_rcytoscape.pdf
GeneNetworkBuilder/vignettes/workflow.eps
GeneNetworkBuilder/vignettes/workflow.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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